+Open data
-Basic information
Entry | Database: PDB / ID: 7y8i | ||||||
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Title | Crystal structure of sDscam FNIII3 domain, isoform alpha7 | ||||||
Components | Dscam | ||||||
Keywords | CELL ADHESION / cell surface receptor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chelicerata (chelicerates) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Chen, Q. / Yu, Y. / Cheng, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis for the self-recognition of sDSCAM in Chelicerata. Authors: Cheng, J. / Yu, Y. / Wang, X. / Zheng, X. / Liu, T. / Hu, D. / Jin, Y. / Lai, Y. / Fu, T.M. / Chen, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y8i.cif.gz | 267.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y8i.ent.gz | 176.7 KB | Display | PDB format |
PDBx/mmJSON format | 7y8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y8i_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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Full document | 7y8i_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 7y8i_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 7y8i_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/7y8i ftp://data.pdbj.org/pub/pdb/validation_reports/y8/7y8i | HTTPS FTP |
-Related structure data
Related structure data | 7y4xC 7y54C 7y5jC 7y5rC 7y6eC 7y6oC 7y73C 7y8hC 7y8sC 7y95C 7y9aC 1va9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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6 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 10919.248 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chelicerata (chelicerates) / Gene: Dscam / Production host: Escherichia coli (E. coli) / References: UniProt: A0A159W468 |
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-Non-polymers , 5 types, 349 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.82 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium dihydrogen phosphate pH 6.5, 18% (w/v) PEG 8000, 3% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 50577 / % possible obs: 99.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 17.58 Å2 / CC1/2: 0.99 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 2452 / CC1/2: 0.665 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VA9 Resolution: 1.9→39.77 Å / SU ML: 0.2025 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.469 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.77 Å
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Refine LS restraints |
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LS refinement shell |
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